Re: SBML survey: should consistency of units be required?
16 Dec '07 14:23
Am 16.12.2007 um 22:06 schrieb <firstname.lastname@example.org>:
> I’m not convinced otherwise yet, but probably I will be when you
> tell me why one of these wouldn’t work:
> d(glucose)/dt = k1*potatoStarch + k2*barleyStarch
> d(glucose)/dt = k1*amylase*potatoStarch/(Kmps + potatoStarch) +
> k2*amylase*barleyStarch/(Kmbs + barleyStarch)
Both these equations work with the current strict specification. If
you do not specify explicitly the units for k1 and k2 they are assumed
to be so that the overall equation has consistent units, which could
be figured out by a tool.
If, however, you do explicitly specify the units of k1 and k2 (the
specification does not force you to do so), they really should be the
right units to make it consistent.
The only thing you cannot do in sbml right now is to write an
assignment rule like "concentration of species A = volume of
compartment C". If you really want to do this you would have to write
" concentration of species A = volume of compartment C * 1", where the
units of "1" are assumed to be so that the whole thing is consistent.
Dr. Sven Sahle
Abteilung Modellierung biologischer Prozesse
Universität Heidelberg, BIOQUANT/Zoologie
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